Cave Story begins with an amnesiac soldier finding a city of rabbits (called Mimigas). The Mimigas are preyed on by an evil doctor, who kidnaps them for his evil experiments. The Mimigas still remember Arthur, a hero from their past and others are awaiting for the return of Dragons. The soldier soon falls in with Sue, a stranger to the Mimigas, but the only one who seems to know about the Dragon Eggs. Unfortunately the doctor wants her next.
Cave Story closely resembles an NES platformer with a distinct 8-bit style and fast gameplay. The main character collects weapons, which level up, and also finds health capsules to increase his life bar. There are a variety of jumping puzzles and boss battles to challenge players as they explore this surprisingly large game.
Rather than a straight port, the Wii version was drastically updated with enhanced and re-drawn graphics, updated character designs, and a new English localization. It also includes a host of additional game modes such as Boss Attack to take on every boss in the game, Sanctuary Time Attack to complete a difficult maze as quickly as possible, and Curly Story where the main character is replaced by the female character Curly. The game also runs in widescreen.